First of all, I have been very impressed by the functionality and abilities of FreeSurfer. I have a question about the longitudinal processing stream.

I have two sets of MRI at two different time points for elderly individuals. Before version 5.1 came out, I ran the first years data through the recon-all step while using version 5.0. Additionally, I made a substantial amount of corrections to many brain regions that I am hoping to not redo (with the number of subjects in my study it will take well over a month or two to re-do this).

I collected my second years worth of data after 5.1 came out, and ran the recon-all on all of these subjects using version 5.1 of FreeSurfer. Similarly, I have already made corrections to this set of data as well.

My ultimate goal is to now use the longitudinal processing stream. I think I understand the process, however, I am wondering if I need to re-do all of my corrections, or if I can salvage my corrections made from previous versions. I am a little concerned about what the -clean flag might do (will it eliminate my corrections?) Furthermore, while looking at your suggestions of editing errors, it says that you can "save time" because some changes only need to be made to the base. However, in my case, I think re-doing all of the edits will actually cost me much more time. I am willing to scrap all of my work if this is necessary, but I am wondering if there is a work-around.